MMSYN1 0776 dkm0713

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Author Information

Dana Murphy

Basic Information

  • ID: MMSYN1_0776
  • Name: smpB
  • Organism: JCVI-Syn3.0
  • Description: This gene is required to handle marking ribosomes for trans-translation [1], or the mediation of ribosomes that have been stalled during the translation process. [2] It binds to tmRNA RNA, which mimics the tRNA shape, and replaces the anticodon stem-loop in a gene with SmpB (tmRNA basically acts like tRNA during trans-translation). [3] Up to three SmpBs can bind to each tmRNA- one binds to the 3' end, the other two bind with the anticodon-like stem region [1]. smpB may also help protect tmRNA from degradation [3] and can act as a less efficient recipient in cell-to-cell plasmid transfers [1]. After the trans-translation occurs, the ribosome is freed to resume regular translation. SmpB is a member of the SsrA tagging complex [1].
  • DNA Length: 447 base pairs.
  • DNA sequence:

ATG TCT GAG CAT TTA ATT GTG AAG AAT AAA AAG GCG TAC TTT AAT TAC GAG ATT ATC CAA ACC TAT CAG GCT GGA ATT GTT CTT AAT GGC CCG GAG ATT AAA TCA ATT CGT AAT CAT GAC GTG AGC ATT AAC GAA GCC TTC GTA CTG ATC CGT AAA AAG GAG ATT TAT ATC CTT AAT ATG AAT GTG AAG AAG TAT CAG TTC GCA AAT TAT ATC AAG GGA CTG GAA GAA ACA CGT ACT CGC AAG TTG TTG TTA CAT AAG AAG GAG ATC ATT AAG ATC CTG AAC AAA ATT AAA CAG GAA AAC TTG ACA ATC ATC CCA GTA AAA CTT TAT TTC AAA AAT GAT TAT GTC AAG TTG GAG ATT GCG TTA GCC AAG GGG AAG AAA TTG CAT GAC AAA CGC CAG ACT ATC AAG AAG CGT GAC ACT GAA CGC AAA GAA CTG AAG GAC TAC AAG TAA

  • Amino Acid length: 148 amino acids.
  • Amino Acid sequence:

MSEHLIVKNKKAYFNYEIIQTYQAGIVLNGPEIKSIRNHDVSIN EAFVLIRKKEIYILNMNVKKYQFANYIKGLEETRTRKLLLHKKEIIKILNKIKQENLT IIPVKLYFKNDYVKLEIALAKGKKLHDKRQTIKKRDTERKELKDYK

Function and Homologs

  • Product: SsrA-binding protein
  • Closest homologous proteins: The top (max three) homologous proteins to this protein, as identified by BLAST searches.
    • SsrA-binding protein [Mycoplasma capricolum], 287/100%/3e-98/99%, WP_011386995.1
    • SsrA-binding protein [Mycoplasma capricolum], 287/100%/3e-98/99%, WP_019269126.1
    • MULTISPECIES: SsrA-binding protein [Mycoplasma mycoides group], 286/100%/7e-98/98%, WP_013447458.1
  • Equivalent E. coli / JCVI functional protein: [EG11782].

Expression

  • Expression Level: Medium
    • Expression Level Hypothesis: The gene is generally called upon when things go wrong, which should hopefully already limit its expression level. However, as many as three SmpBs are used to mediate each stalled ribosomes, which could explain why it has a medium expression level rather than a low one.
    • Expression Level References and Description: Data from the file EcoliProteomicExpressionData
  • Expression Time: Late
    • Expression Level Hypothesis: This gene's function is to fix things. It is only needed when other functions like translation have been running long enough to falter.
    • Expression Time References and Description: "analysis of affinity purified tmRNA·ribosome complexes also suggested the presence of only one SmpB molecule at a late stage of the trans-translation process" [source]


Gene Context

  • Other Components: tmRNA
  • Possible Dependencies: tRNA modification
  • Reactions: tmRNA + smpB(1-3) = tRNA [source]
    • Inputs: tmRNA, smpB
    • Outputs: tRNA

Construct

  • Synthesis Score: The synthesis score of your construct: 1, 2,3
  • Predicted Translation Rate: Prediction of construct translation rate from the RBS calculator
  • Design Notes and Details: For example, had to use a rare codon to fix folding energy;
  • GenBank File: A link to the GenBank file. file